Unknown DNA
by Kie Santiago
Summary: Beckett and Castle investigate the murder of a Transgenic. Total AU. How will they react to the news? Where will their investigation turn? Will they finally come to terms with their feelings for one another?
1. Chapter 1

**Summary: **Beckett and Castle investigate the murder of a Transgenic. Total AU. How will they react to the news? Where will their investigation turn? Will they finally come to terms with their feelings for one another?

**Author's Note: **Hey guys! This is my first Castle Fanfic. If they are not totally in character, just understand that this is FICTION. Hopefully, I will do them some justice however. This story has been in my head for a few days now.

By the way, has anyone seen the sneak peaks for To Live or Die in L.A.? The one in their hotel suite? Can anyone say OH EM GEE? I'm depressed because I have class that night but I will be sure to watch it the next day.

Please R & R. Let me know where you'd like to see this story go.

**Disclaimer: **I do not own Castle and their characters.

Unknown DNA

_RRRRRIIIIINNNNNNNGGGGGGGG!_

The shrilling sound of her cell phone startled Detective Kate Beckett from her much needed slumber. For the last two weeks, she had been on an extremely frustrating case. Just yesterday morning, they managed to catch the killer and have a confession by the end of the day. It was a relief to the entire team so they all went out for celebratory drinks at the Old Haunt and retired by 11:30pm.

Lifting her head up to take a peak at her alarm clock, she noted that it was only 3:37am. She reached over to the nightstand and fumbled with her phone before pressing it to her ear on the third ring.

"Beckett."

She said with an incredibly sleepy voice.

"_We got a case."_

The detective groaned in response and wrote down the address before hanging up. Her head flopped back in frustration, pulled a pillow to her face, and screamed in it. Normally, after a particularly hard case, the team was given a few days off. So why were they calling only hours later?

Yawning and stumbling out of bed, she made her way to the bathroom to get ready. Within 20 minutes, Beckett was dressed and securing her gun in its holster. She ran her fingers through her hair to tame the mane before finally putting on her mother's necklace along with her father's watch.

Beckett contemplated whether or not to call Castle. He barely had any chance to sleep, having stayed with her whenever she remained at the Precinct well past midnight. He took care of her, knowing that she sometimes forgot to eat when a case was too rough. She was dedicated and committed to finding the truth. Over the last few years, she's come to depend on Castle's presence. He was her bright light at the end of a very dark tunnel. He made her job a little fun and has been surprisingly insightful into the criminal mind. She trusted him as her partner and with her life but did she trust him with her heart?

Opting to give him a call, she pulled out her phone and hit number '1' on speed dial.

"_Mhm Castle."_

He said sounding groggy and barely awake.

"Hey Castle. We've got a case."

Beckett instantly regretted calling him. She knew how little time he has spent with Alexis and his mother. His lack of sleep was beginning to wear on his, much as it has on her.

"_What? Already? I thought you had the weekend off?"_

"Crime doesn't stop just because we would like to get more sleep. Listen, if you don't want to co-"

"_I'll be there. Just text me the address."_

Kate could not help but smile and slide the phone back into her pocket. Despite everything, Castle was reliable as ever.

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Stepping out of her car, Beckett caught sight of Castle heading her way with two Styrofoam cups of coffee. Green eyes looked into his blue ones with so much gratitude.

"How do you get here before me _and_ with coffee? Thanks."

She said before bringing the cup to her mouth. She tested the temperature quickly before taking a large gulp of the much-needed cup.

"What can I say Detective?"

They then both turned and headed over to Lanie who was kneeling next to the victim. A dumpster was pulled away from the brick of an apartment building.

"What've we got?"

"Caucasian male, mid to early twenties."

"He's just a kid."

Castle said with a hint of sadness. He could not be much more then 6 years older than Alexis. The victim was wearing a black shirt, a leather jacket, and jeans. He suddenly felt the urge to go home and hug his daughter but brushed it aside.

"Cause of death?"

He asked.

"From what I can tell, a broken neck. Based on the temperature of his body, I'd say it happened between 11:30 pm and 1 am."

Lanie took a moment to glance up at the two of them, wondering why they were requested to be on the case. It seemed fairly standard.

"ID?"

Beckett asked. Just then Ryan and Esposito walked up and stood by Castle.

"No wallet or ID. Residents said they did not hear nor see anything. Could be a robbery gone wrong."

Castle then knelt down next to the body as well, staring at the clearly broken neck. His eyebrows furrowed as he got the look that something did not add up.

"What?"

Kate asked, all too familiar with that look.

"How strong would you have to be break a neck nearly in half and almost rip the head off?"

"What are you getting at Castle?"

"You'd have to be pretty strong. The head looks as if it was almost completely taken off the body. He's extremely healthy looking and strong. I'd say the military judging by his haircut and physique."

"The bruising on his neck would suggest that someone's hands might have done the job. But I will know more when I get him back to the morgue."

Lanie cut in before Beckett then turned to the two detectives.

"Who found him?"

"Homeless guy, Fred Miller. Found the body behind the dumpster when he was digging through the trash."

"Anything else?"

She directed her question to Lanie. When she shook her head she turned from the body and back to Ryan and Esposito.

"I want to talk to Mr. Miller. Send uniforms to canvass the area to see if anyone saw anything out of the ordinary. Look through missing persons and see if we can ID our vic."

"Right on it."

Ryan said before they both left. Castle then turned to Beckett.

"I don't get it. Why would they call you in for this?"

"I don't know Castle. Come on, let's talk to Fred."

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_Author's Note: I should have the next chapter soon. Hopefully, it will be much longer! Don't forget to make my day and review! Also, if anyone wants to gush about "Caskett" just send me a message :D_


	2. Chapter 2 So Weird

**Summary: **Beckett and Castle investigate the murder of a Transgenic. Total AU. How will they react to the news? Where will their investigation turn? Will they finally come to terms with their feelings for one another?

**Author's Note: **Yay! I'm so happy that you guys like the story and have put it in your alerts. Thank you for the support. The beginning will be a little slow at first but I promise the storyline will pick up.

I was totally screaming when I saw Castle go back into the room in the last episode

Please R & R. Let me know where you'd like to see this story go.

**Disclaimer: **I do not own Castle and their characters.

**Chapter 2**

So Weird

Beckett and Castle headed over to where the homeless man was standing. His back was leaned up against the brick building. His eyes darted back and forth while his hands wrung the bottom of his shirt nervously. He was about 5'7", African American, thin, and with a long beard. His clothes were worn and tattered with stains of dirt and grime on them. His hair was nappy and it seemed as though it had not been washed in weeks. Overall, he appeared completely worn down.

As they stepped closer, Beckett noticed the glassy look in his eyes. He was clearly afraid and paranoid of something or someone.

"Fred Miller, my name is Detective Kate Beckett and this is my partner, Richard Castle. Can you tell us how you found the victim?"

He turned his dark eyes to look into her green ones and appeared to contemplate his answer. He remained silent for a good 15 seconds before heaving a deep sigh and fidgeting.

"I….uhhh…. come here a lot. These folks leave good stuff sometimes. Oh!" Fred's eyes suddenly widened with a moment of glee. " Like one time I found a leather jacket. Can you belie-"

"Mr. Miller, please answer the question." Her voice was serious and to the point.

"Oh right. So I was diggin' around this dumpster here and as I was backing away, I saw something. And then bam! There he was…" He appeared to have drifted off in thought and stilled his hands.

"About what time was this?"

"Sometime after 3."

"Did you see anyone at all in the alley?" Asked Castle quickly.

Shaking his head, "Nah usually no one comes back here unless throwin' out the trash. Do you think he will come after me? What if he saw me?"

"I wouldn't worry too much, Mr. Miller. If you see or remember anything else, please give me a call."

Reaching into her coat, Beckett pulled out a business card and handed it over to the dirt-covered man. His dark hands reached out and grabbed the card before placing it in his side pocket. She then turned and started heading for her car with Castle close on her tail.

"So…what next?"

"We head to the precinct and see if Ryan and Esposito found something."

The detective then stepped into her car and slammed the door shut.

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Castle and Beckett walked into the 12th Precinct to find Ryan and Esposito sorting through a mound of missing person files.

"Anything?"

Beckett asked. Without glancing up, Ryan answered.

"Not yet. We checked missing persons from this week but no hits. We are now looking through….wait I think I found something."

Leaning over, Esposito took a look at the file while Beckett and Castle leaned in as well.

"Zack Nicholes. His girlfriend….Andrea Sill reported him missing 2 weeks ago."

"2 weeks?" Castle said, attempting to speed read over Ryan's shoulder. "Why would they wait 2 weeks to kill him?"

Beckett took a moment to glance down at her father's watch. It was a little past 5:45am. Ignoring Castle's question, she thought about their next move.

"Alright. Lets call in the girlfriend and see if she can shed any light. Ryan, pull his financials and check if anything stands out. I'm going to head down to the morgue."

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Castle had opted to stay behind for a change to set up the murder board. He was really beginning to turn more into a cop ever day that passed by. The last few years of shadowing Detective Beckett had really changed him. He was much more mature and worked well with the team. Of course Kate still referred to his as a 5 year old on a sugar rush. Though at the end of the day, he was her lifeline. He brought her back to reality whenever she dove a little too deep in a case. He made sure that she took care of herself when she'd forget to eat. She brushed through the double doors to see her best friend examining the victim.

"Hey Lanie, got anything?"

"Hey where's your shadow?" Lanie looked up from leaning over the body.

"He's with the boys. What did you find?"

"Not much. I can tell you more when I finish his autopsy. I do know that he was extremely healthy. He has no imperfections, amazing teeth, and very fit. Someone would have to be _very_ strong to take him down. The bruising on the neck is consistent with strangulation. He may have been held there before the neck was broken."

"Any idea how his neck was nearly torn off?"

"That's the weird part. I found nothing that could account for that type of injury. I know this sounds crazy but if I had to guess, I would say someone did it with their bare hands."

"So weird." Kate said while her eyebrows furrowed.

"I know girl. I will also run some blood tests and see if he'd been sedated. As I said, he was very fit. It would take a lot to keep him down."

"Okay thanks Lanie. Call me when you find something."

With a wave, Beckett headed out of the morgue. _So weird…._

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_Authors Note: Pleaseeeee review :D Again, I know it's a slow start but it will pick up ^^_


	3. Chapter 3 Notification

**Summary: **Beckett and Castle investigate the murder of a Transgenic. Total AU. How will they react to the news? Where will their investigation turn? Will they finally come to terms with their feelings for one another?

**Author's Note: **Sooooo sorry for the wait!

Please R & R. Let me know where you'd like to see this story go.

**Disclaimer: **I do not own Castle and their characters.

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**Chapter 3**

Notification

Beckett returned back to the bullpen shortly after leaving the morgue. The soft ding of the elevator signaled her entrance while she strode out of the sliding doors, looking for her partner. Her soft eyes soon lay upon his hunched form and noticed Castle was still diligently putting together the murder board. The marker squeaked as he swiftly added every piece of information they gathered thus far. It was one of the few times that he'd been ever allowed to do the murder board so he took his work incredibly seriously. Kate studied him with interest as his brow furrowed while stopping mid-sentence. He then resumed after a thought. It was almost as if the tables had been turned. Her staring while he worked. Despite having no formal training, Castle was as good a 'cop' as the other Detectives, if not better, more insightful, at times.

"Now look who's being creepy?"

Castle said as he finished writing. He gently capped the marker and placed it down before turning toward his favorite Detective with a smug smile. She merely smirked before standing next to him to read over the board. They both checked it over with ease, looking for any mistakes and finding none.

"Not bad Castle." She commented before leaning against her desk.

"Did I just hear praise Detective?" His boyish smile almost caused her to laugh but she hid it with a well-timed brush of her hand over her mouth. She then quickly rolled her eyes at him.

"So what did Lanie say?" He continued, leaving the playful banter for a moment.

"She said our vic really maintained his health. He was pretty fit which may suggest a military background. Lanie isn't sure how his neck could have been snapped or pulled so roughly as there are no other signs of a possible murder weapon. The only thing she found so far is bruising from where our killer grabbed him."

"What if…." Castle starts. "The CIA trained an assassin and he went rogue. Maybe they killed him."

"Really Castle? I hardly think the CIA is involved." A case would not be right if it did not include one of the writer's infamous CIA theories.

"One of these days, I will be right. It's just a matter of time. Plus, it would make for a great story."

"Castle, this isn't one of your books. Sometimes, the truth is really not so devious."

The back and forth between writer and Detective probably could have gone on for hours. It was familiar, light, and safe. Moments like these proved how beautifully in sync they were and how this was their own private way of communicating. They both secretly loved to argue. It brought the gruesome nature of these crimes from depressing the police officers that investigated them. He brought humor to a normally dark situation and for that, her team was eternally grateful.

Beckett ended the conversation from continuing by walking toward the break room. Today, she was going to need coffee….lots…of coffee. Before she could reach the entrance, Castle had already beat her to it and offered to bring it to her while she filled in the new information from Lanie on the board. Nodding briefly, the Detective headed back, lifted the cap off, and started to fill in what little they now knew. The dry-erase marker glided smoothly and only moments later, Castle returned, handing her the warm cup. The tiniest of smiles pulled against the corner of her mouth before reveling in the feeling of the hot liquid slipping down her throat. She made a small noise of approval before stepping back to her desk.

They stood there in silence, looking over the board again and again, hoping that something, anything, would lead them to answers.

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"Victim's girlfriend just arrived."

Esposito said, walking up to the pair. The sound of his voice jolted her out of her thoughts. She looked down at her father's watch. 8:23am. _Where did the time go?_

"Okay. Lets see what she has to say. Come on Castle."

Her partner eagerly popped up from his seat and followed after her. Notifications were always hard, especially for Beckett. Each time, she remembers the loss of her mother and how she felt when she'd been told that she was murdered. Now, as a Homicide Detective, she was forced to do the very same thing. She would never tell him this, but Rick made it all that much easier. His mere presence was a comfort and he knew how to stay quiet at all the right times. He understood that a notification was serious and no laughing matter.

Walking into an office, Detective Javier Esposito led the distraught woman to sit down before exiting. On his way out, he passed the pair, heading off to go check on Ryan and see if he had any new leads. Her red rimmed, teary eyes met Detective Beckett's first before glancing into Castle's as he sat down beside his partner.

Andrea Sill, the victim's girlfriend, feared the worst. The look in their eyes told her that they knew something in regards to Zack.

"D-Did you find him?" She asked.

"Ms. Sill, my name is Detective Kate Beckett and this is Richard Castle. I understand you were in a relationship with Zack Nicholes. When was the last time you saw him?"

Beckett tried to avoid her question for the moment. Sometimes, it was best to ask questions before the official notification. When others found their loved ones have been murdered, their emotions often impeded on the actual investigation.

Andrea wanted to help but cautiously answered.

"Um it was about two weeks ago. I was so happy to see him but he seemed…worried."

"About what?" Castle gently asked.

"He didn't say. I missed him so much and he just got back…." Her voice trailed off as she remembered how happy she had been to see him. Her eyes welled up with tears again.

"Andrea what did he do for a living?" Beckett followed.

"He was in the Marines. He had just got back from Iraq. He's been gone for 6 months."

"How long have you two been together?" She continued.

"2 and half years. What happened to him? Why are you asking me all these questions? Do you know where he is?"

"I'm sorry to inform you but Zack's body was found earlier this morning."

Andrea simply gasped, as her worst fears became reality. Her hand quickly lifted to her mouth and her body shook with heartbreak. After two and a half years, the love of her life was gone forever. She was completely absorbed in her grief and hadn't even noticed when Kate reached across and grabbed her hand to comfort her. She knew all too well that very little would help but she had to at least try.

"I'm so sorry. We are going to try out best to find those responsible for his murder."

Beckett barely received a nod from Andrea before she suddenly realized something.

"Oh gosh! His parents. They don't know!"

"Do you know a way we can contact them?"

"Um…yes…here let me get you their number. They live in New Jersey." She sniffled while reaching into her purse to pull out her phone. Andrea's hand tremored while scrolling through her contacts looking for their familiar names. Castle leaned over to give her a tissue. She graciously accepted the offer before writing down the names and phone numbers of his mother and father.

"Thank you Andrea. If you remember anything else, anything at all, or if you need to talk, here is my number."

Beckett handed her a business card before standing up. Castle had remained mostly silent for the entire interview. He stared with sadness for several moments before walking out behind her.

Moving briskly, Kate bounded toward her desk.

"Ryan I need you to run financials on our vic. See if anything pops."

"On it boss."

"Okay so he's a marine which supports the theory of military background. I wonder if he had bad blood with anyone or if he made any enemies during his time served. Esposito, I want to know about all his known associates. Andrea said something was bothering him and we need to find out what it was. See if anyone from his platoon knows anything about it. Castle and I will run down these numbers and get in contact with his parents."

Esposito turned and headed for his desk to start making phone calls. Two notifications so early in the day? She could already tell this was going to be one hell of a case. _So much for sleeping._


	4. Chapter 4 Wait What?

**Summary: **Beckett and Castle investigate the murder of a Transgenic. Total AU. How will they react to the news? Where will their investigation turn? Will they finally come to terms with their feelings for one another?

**Author's Note: **-Sad face- No reviews on the last chapter. I hope this one is a bit better for you!

Please R & R. Let me know where you'd like to see this story go.

**Disclaimer: **I do not own Castle and their characters.

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**Chapter 4**

Wait what?

Kate Beckett watched as her two favorite Detectives left to do there given tasks. Her hand rose to grab her desk phone but paused. She hated this. It was the one aspect of her job that always seemed to jolt her. Every notification to friends and families meant that she was destroying their world with her news. Their lives would forever be changed the moment the words left her mouth. She remembered how much her life was impacted by the loss of Johanna Beckett. The stench of liquor still haunted her when she thought of her father's path into a dark place where he almost never made it out. She remembers her own descent when she crept into her mother's murder. And to this day, she wonders if she will ever be free of the burden that lingered there in the background. Her entire life was circled around a single notification. How would this affect theirs?

Castle seemed to sense her hesitation and gently laid a hand on her shoulder. She snapped out of her thoughts and lifted the phone as he removed it. She appreciated the gesture but did not make a habit of pulling affection and comfort from her partner. Just him being there was enough to give her the strength to go on. Without ever having wanted it, she became to depend on him. He was the light at the end of a very dark tunnel.

The phone rang several times before an answering machine picked up. Sighing, she waited for the beep and left a simple but effective message.

"Mrs. Nicholes, this is Detective Kate Beckett with the NYPD…"

After finishing the message, she replaced the phone and was about to say something before frantic footsteps came right her way. The Detective turned her head in surprise as Lanie came rushing to her desk.

"Kate! Someone stole the body!"

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"Wait what? Lanie, slow down. What do you mean someone stole the body? I was just there."

Lanie took a deep breath before explaining what happened only moments earlier. "I left the autopsy room to use the bathroom. And when I returned, everything was gone. Kate, I didn't leave for more than 4 minutes. How the hell could someone have not only cleared out the body but all of my notes as well? Everything is gone. I…"

The look on Castle's face was priceless. He was shocked but there was a gleeful excitement as well. This case was turning completely crazy and that was enough to make him giddy. Leave it to Castle to find the joy in a missing body. This could completely ruin everything and he was sitting there in complete awe.

"And you were saying my theories were crazy…I must say Beckett, it sure seems like a CIA cover-up to me don't you think?"

Instead of her normal quip or reprimand, she merely sat there in shock. 4 minutes. That was barely enough time to grab the files and definitely not enough time to remove a body from the lab.

"They must still be in the building."

She quickly turned and grabbed her phone again.

"This is Detective Kate Beckett, badge number 0334. We need to lock down the building. No one gets in or out!"

Kate practically slammed the phone down and bolted out of the chair and headed straight for Montgomery's office. He was just getting off of the phone when she entered his office in a flurry.

"Sir-"

"Beckett, I know. I just sent out uniforms to search the building. If they're still inside, we will find them. I want you to go down to the lab and see if you can figure out how the hell they got in there without anyone noticing. Have Ryan review the cameras and check to see if they caught anyone coming in or out."

"Yes sir."

Essentially, without the body of Zack Nicholes, their case would become a dead end. His autopsy was crucial to understanding how he died and who may be behind it. While Castle seemed to enjoy the sudden excitement, she took this as a major blow. What was she going to tell the boy's parents? Hadn't she just left them a message to call her back? What if they came in for their notification before the body was recovered? Everything about this case made her head hurt and she felt a wave of nausea. The lack of real food or sleep and the extreme stress from the case was literally making her sick. Rushing passed her desk; she practically dragged Castle toward the elevators.

"Whoa whoa whoa Beckett! I think I'm capable of walking on my own." Castle said with a slightly amused expression.

She pushed him into the elevator and hit the down button multiple times before the door started to slide closed. She then spun to face him with fury in her eyes. All of her pent of frustration was about to be unloaded on her partner.

"You just don't get it do you Castle? A boy was murdered, not much older than Alexis. And now, right before I tell his parents that their son has been killed in one of the most brutal ways possible, his body is stolen. You're seriously taking this as some kind of joke?"

Beckett's voice started to rise with each word. The enormity of the situation began to make way into Castle's brain and his smile faded quickly. His eyes shifted down with guilt and shame for his actions. Normally, Kate was used to Rick's antics, but at this moment, she just couldn't take it anymore.

"You're right."

He was suddenly bombarded with thoughts of his beautiful, red-headed daughter, Alexis. Her happy spirit and intelligence could brighten anyone's day. He couldn't imagine life without her and now, he felt guilty for having taken part in downplaying the enormity of the situation at hand. Stepping off of the elevator, he followed behind Kate with newfound focus. His eyes started to scan every crevice until they made it into the lab. Lanie was frantically looking around the office for any trace of the victim or her files.

Several other officers joined in on the search of the morgue, looking in closets, testing vents for any possible breaks, and opening any large bins, boxes, or garbage cans for places to hide a body until it was safe to exit the building. It almost seemed like a lost cause until Castle noticed the tiniest white edge of a business card. He lifted the piece of stock between his fingers where a simple symbol was imprinted dead center in all black ink on the card. The image was that of a DNA strand with a flame at the base.

"Hey Lanie, does this look familiar to you?"

Both Lanie and Beckett looked up and came over to take a peek at the card. The Medical Examiner looked confused but Beckett's hand came out softly and touched the symbol. She stared, saying nothing but simply pushing her eyebrows together in deep thought. All of a sudden, recognition drifted onto her face.

"I've seen this before…"

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_Authors Note: Short chapter! More to come! Please review ^^ What would you like to see more of?_


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